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<div class="title">moltk::Alignment_&lt; SCORE_TYPE &gt; Member List</div>  </div>
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This is the complete list of members for <a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a>, including all inherited members.<table>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#a1cf784f435f461b69d2cb6fed194e1c8">align</a>(const Alignment_ &amp;, const EString &amp;, const EString &amp;) const </td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#af92538fd947d2503ecd35984642b875c">Alignment_</a>()</td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#a3aebdf39421b1cd2b446a7f23e2209c8">Alignment_</a>(const Biosequence &amp;sequence)</td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#adc92236397e52158d76469813909b6f1">Alignment_</a>(const std::string &amp;alignment_string)</td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#a76eab18197656efd9ef9c5c3c1b68307">Alignment_</a>(const char *alignment_string)</td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#a6aa429375949cd6c7fd4b58960afcc7b">append_sequence</a>(const Biosequence &amp;sequence)</td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#a67e797edd272010b8e6f7845b825acf4">EString</a> typedef</td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#a64ffedc0eba04a1a80c349a757275b35">fasta</a>() const </td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#a3408c640ccc854b0b9af7a593521186a">get_estring</a>(size_t index) const </td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#ac113e59bf55f00ffd7957a39b0d13f5c">get_number_of_columns</a>() const </td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#a53d9faa384258178abd19592740deda6">get_number_of_sequences</a>() const </td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td><code> [inline]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#aefff61528a8a3210501ee4e517c485b6">get_pretty_width</a>() const </td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td><code> [inline]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#a14c87e3b0fbf3fc6ddaffb74f18aa539">get_score</a>() const </td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#a3320970bfee0ea1058c5a75632fa56b0">get_sequence</a>(size_t index) const </td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#a03fb9aaf5c82353cb7152364542654d9">id_table</a>() const </td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#ae82e4fe2134fecfa374499781ec3d2d8">List</a> enum name</td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#ae82e4fe2134fecfa374499781ec3d2d8a3a38c67cfd20916ed2aca72d487e4eb8">LIST_SEQUENCE</a> enum value</td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#ae82e4fe2134fecfa374499781ec3d2d8aed118ee80047d7db2b9148f435540686">LIST_STRUCTURE</a> enum value</td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#abfd24b91e6307001f8268a8b95a78fb1">load_fasta</a>(std::istream &amp;input_stream)</td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#a1f9c611fce627e732ba98b4c6bbe7418">load_fasta</a>(const std::string &amp;file_name)</td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#a685b48576e005de9013fea1c1457814c">load_string</a>(const std::string &amp;alignment_string)</td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#ac929115e5fbbfb6a16f537f0d024ff72">m_score</a></td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td><code> [protected]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#a8618745ccb54c7588fa56cfc1f264d3a">operator&lt;&lt;</a>(std::ostream &amp;os, const moltk::Alignment_&lt; SCORE_TYPE &gt; &amp;ali)</td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td><code> [friend]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#ada1e80499e1d31106f1b319f233b3c60">pretty</a>() const </td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#a7b353afe4712a512a87f5ef9e61af88c">pretty_width</a></td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td><code> [protected]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#a825baa50931639decf5b6989801412f2">repr</a>() const </td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#a468e2e5c2a46fb3b163805942a533c08">rows</a></td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td><code> [protected]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#afb22dd1d74614d10f0633ce8bfb2f6a6">sequences</a></td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td><code> [protected]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#a0a7ba36b2af5bc886e8bcbc4fbdb4400">set_pretty_width</a>(int width)</td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td><code> [inline]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#a42cec9b9709afe53383953f3f687d16c">set_score</a>(const SCORE_TYPE &amp;s)</td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#ab7ef21f5246cf6aeeb64e199d02ff8fa">structures</a></td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td><code> [protected]</code></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#ae92aea8bd71e9af1918cebda993da208">write_fasta</a>(std::ostream &amp;output_stream) const </td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#a5b1d1fd583e2843f594dda8f8e85f3c3">write_fasta</a>(const std::string &amp;file_name) const </td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#a3e3b0dbdb6593e6446ea92a21f5af53c">write_id_table</a>(std::ostream &amp;output_stream) const </td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#a0d0e9fb7403c1f7962109d4fe3e26239">write_id_table</a>(const std::string &amp;file_name) const </td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#a530d9e4e4b1c3d1334d6db811a299f10">write_pretty</a>(std::ostream &amp;output_stream) const </td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#ae154886908be0688f8a3396cce3f618b">write_pretty</a>(const std::string &amp;file_name) const </td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td></td></tr>
  <tr class="memlist"><td><a class="el" href="classmoltk_1_1Alignment__.html#a96e7fab5bcacdb8c9f1fa2b272cd3dc2">~Alignment_</a>()</td><td><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_&lt; SCORE_TYPE &gt;</a></td><td><code> [inline]</code></td></tr>
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